Dear Justin
Very thanks for your reply.
You said I suspect your Gromacs version is somewhat outdated, as recent
versions account for periodicity when
making this check. I used 4.5.5 version of gromacs. What version of
gromacs is more appropriate for my case.
Based on your suggestion, I used
Dear GMX users,
I have a question about the combination of the installation parameters. I
compiled the fftw lib with --enable-sse2 and configured the gromacs with cmake
.. -DGMX_CPU_ACCELERATION=SSE4.1. I'd like to know if it is ok to use such a
combination?
Many thanks.
Mingjun--
Hi,
On Sep 16, 2013, at 11:23 AM, mjyang mjy...@hku.hk wrote:
Dear GMX users,
I have a question about the combination of the installation parameters. I
compiled the fftw lib with --enable-sse2 and configured the gromacs with
cmake .. -DGMX_CPU_ACCELERATION=SSE4.1. I'd like to know
Dear Justin
About following warning in grompp using
WARNING 1 [file em.mdp]:
The sum of the two largest charge group radii (6.940482) is larger than
rlist (1.20)
You said You probably have molecules split across PBC in the input
coordinate file. here's nothing wrong in that case
I mention
Dear all
I would like to calculate the standard deviation (as the error bar) for
dV/dlanda.xvg file. I used g_analyze command as the following:
g_analyze -ffree_bi_0.9.xvg -av average_0.9
I got:
set average *standard deviation* *std. dev. /
sqrt(n-1)
On 9/16/13 7:37 AM, shahab shariati wrote:
Dear Justin
About following warning in grompp using
WARNING 1 [file em.mdp]:
The sum of the two largest charge group radii (6.940482) is larger than
rlist (1.20)
You said You probably have molecules split across PBC in the input
coordinate
On 9/16/13 3:06 AM, shahab shariati wrote:
Dear Justin
Very thanks for your reply.
You said I suspect your Gromacs version is somewhat outdated, as recent
versions account for periodicity when
making this check. I used 4.5.5 version of gromacs. What version of
gromacs is more appropriate for
On 9/16/13 9:47 AM, shahab shariati wrote:
Dear Justin
My input coordinate file is a gro file (sys.gro). When I visualize that by VMD,
all things is ok and true.
After minimization, I obtained a gro file (em.gro). When I visualize that by
VMD, About 5 DOPC molecules leave bilayer structure
Dear Justin
Very very thanks for your quick reply.
The sys.gro file is positioned within a box that is too large, a fact that is
easily observable in VMD. I suspect that the void space results in
instability.
If I positioned system in a smaller box, my problem (instability) solved ???
On 9/16/13 10:52 AM, shahab shariati wrote:
Dear Justin
Very very thanks for your quick reply.
The sys.gro file is positioned within a box that is too large, a fact that is
easily observable in VMD. I suspect that the void space results in instability.
If I positioned system in a smaller
Dear Justin
Very very thanks for your quick reply.
The sys.gro file is positioned within a box that is too large, a fact that is
easily observable in VMD. I suspect that the void space results in
instability.
If I positioned system in a smaller box, my problem (instability) solved ???
Hi,
I'm attempting to build GROMACS 4.6.3 to run entirely within a single Xeon
Phi (i.e. native) with either/both Intel MPI/OpenMP for parallelisation
within the single Xeon Phi.
I followed these instructions from Intel for cross compiling for Xeon Phi
with cmake:
Hello. I was calculating the viscosity of hexane through the Gromacs
command g_energy. Three files are generated: visco.xvg, evisco.xvg and
eviscoi.xvg. The file visco.xvg presents the shear viscosity and bulk, but
the value does not match the experimental. I used 8 ns simulation at
equilibrium.
I am sorry for the late follow-up on this subject.
My results using PME electrostatics do not show any differences between
versions 4.5.4 and 4.6.3 (I also checked with 4.6.1 and it gave the same
results):
https://www.dropbox.com/s/o2kswrw5eq8fcsp/plot_batch-1_pme.png
I hope that you, Niels,
Hello,
On Sun, Sep 15, 2013 at 5:05 PM, Venkat Reddy venkat...@gmail.com wrote:
I found g_sgangle is the suitable tool
to calculate the angle between two cholesterol rings. But the problem is, I
want to do this analysis for my whole system, which has 40 cholesterol
molecules. Whereas I can
On Mon, Sep 16, 2013 at 7:04 PM, PaulC paul.cah...@uk.fujitsu.com wrote:
Hi,
I'm attempting to build GROMACS 4.6.3 to run entirely within a single Xeon
Phi (i.e. native) with either/both Intel MPI/OpenMP for parallelisation
within the single Xeon Phi.
I followed these instructions from
This is the command I used
pdb2gmx -f protein.pdb -o processed.gro -water spce -ignh
And I used OPLS-AA/L all-atom force field..
--
View this message in context:
Hi Santhosh,
Try renaming the atom (mind the space):
sed 's/OXT/O2 /' pdbfile fixed.pdb
And then run pdb2gmx on that.
Cheers,
Tsjerk
On Tue, Sep 17, 2013 at 6:05 AM, Santhosh Kumar Nagarajan
santhoshraja...@gmail.com wrote:
This is the command I used
pdb2gmx -f protein.pdb -o
Thank you sir for the nice tip. I will try it out and let you know if I
have any problem.
On Tue, Sep 17, 2013 at 12:38 AM, Teemu Murtola teemu.murt...@gmail.comwrote:
Hello,
On Sun, Sep 15, 2013 at 5:05 PM, Venkat Reddy venkat...@gmail.com wrote:
I found g_sgangle is the suitable tool
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